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Showing content from https://github.com/bpp/bpp/releases below:

Releases · bpp/bpp · GitHub

Releases · bpp/bpp

• usedata=2 for using fixed gene trees as data instead of sequences
• Simulation of sequences with genotyping errors with mixed diploid and haploid
  sequences
• Command-line option --keep-label

• Number of digits in a1b1 file
• Printing inf for Effu and c if Effy=1
• Alingments from compressed site patterns are now written in separate file

• Crash due to mismatching header line in a1b1 file
• Order of sampling W values in a1b1 file
• Theta pjump calculation for mixture of gibbs and sliding window sampling by
  introducing move counters for each eps
• Incorrect number of steplengths when using --theta_mode 3 under MSC-I model 3
• Heredity scaler estimation when combined with gibbs sampler for thetas
• Incorrect typecast in diploid code when tipdating

• thetaprior: always estimate theta with invgamma prior unless 'int' specified
• invgamma theta prior requires that a>2

• duplicate logging of a1,b1 for theta and w under certain conditions
• logging a1,b1 for phi even when sliding window is used
• SNL move assertion fails with thetas integrated (called old density function)

• a1b1 summary handles missing data
• per-locus affected lists for extended rubberband algorithm
• finetune option to use dictionary-like syntax

• logging of a1,b1 parameters of theta conditionals when thetas integrated out

• -nan for th1 caused by having one sequence per species and differnt step
  lengths for inner and tip nodes
• logging a1 and b1 for W parameters
• theta distribution flag when summarizing conditional a1b1 file
• when running --summary the conditional a1b1 file was being overwritten

• Re-parameterization of the MSC-M model (M to w)
• Summary statistics output format (transposed, aligned, parameters enumerated)
• Summary for both w and M (MSC-M model)
• Prior for HKY and K80
• Only summarize unique theta parameters
• Removed unnecessary sorting in several proposals
• Replaced outfile and mcmcfile with a single jobname option
• All output filenames now begin with string defined in jobname option
• SeedUsed no longer created when invoking BPP without parameters

• Gibbs move for sampling theta from conditional distribution
• Gibbs move for sampling phi from conditional distribution
• Gibbs move for sampling w from conditional distribution
• Linked theta model for MSC-M
• PDF visualization of species tree (MSC and MSC-M models)
• Posterior summaries for parameters whose conditionals are tractable or can
  be approximated
• Ported likelihood calculations for aarch64 neon instructions (apple silicon)
• Option --extend to extend runs by additional MCMC steps
• Options --phi-slide-prob and --theta-slide-prob to control the frequency of
  phi and theta sliding window moves

• Option of integrating out thetas with linked theta models
• Theta model "linked-msci" when a branch is broken into three or more segments
• Illegal memory accesses when constructing faketree under linked theta models
• Fixed efficiency calculation routine, added rho1 in output

• Example data
• Extended rubberband move is now the default move for MSCM

• Pseudopriors for migration rates
• Option to specify a separate prior for each migration rate
• Per-locus variable migration rates
• Reversible-jump MCMC move for adding and removing migration rates
• Move to flip the direction of a migration rate
• Option to change the probability of using a gibbs sampler vs sliding window
  proposal for theta moves (default: 0.2 sliding window)
• Option for having one stepsize per theta parameter
• Option for having one stepsize for tip nodes and one for inner nodes
• Option for disabling core pinning

• Memory leaks
• Invalid access of migbuffer structure in theta gibbs proposal
• Binary mode when opening checkpoint files

• Default theta proposal to the original sliding window move
• Default number of thetas on monitor output set back to 3

• Gibbs sampler for thetas with t1/t4 conditions

• Typos

• Number of thetas,taus,phis and mrates on screen output

• Gibbs sampler for migration rates

• Priors on frogs example control files

• Disabled twin towers unidentifiability algorithm when not using data
• Printouts from label switching algorithm are now included in output file
• Gibbs sampler is now the default move for thetas

• Crash when resuming from checkpoint due to uninitialized IM variables
• Checkpointing when using linked theta models
• Copying of linked_theta attribute when cloning snodes -- fixes linked theta
  models under IM

• Consistency checks for tau definitions in --simulate
• Error when using MSCi and IM together
• Possibility of displaying multiple phi means on screen output
• Gibbs sampler for thetas under MSC,MSCi,IM with gamma prior

• Shortened MSci model information table

• Crash when resuming from a checkpoint with SNL enabled
• Assignment of mean phi values for model B on summarized species tree/network
• Position of theta and tau in the header of the last output table

• Option --summary for only summarizing the MCMC file
• Algorithms CoG0,CoGN,BetaGamma for resolving identifiability issues
  associated with BDI events

• Phi parameters (MSCi model) for non-BDI events always correspond to
  horizontal edges. If both parental edges of a hybridization node are
  horizontal or both are non-horizontal, then the phi parameter always
  corresponds to the mirror node.
• Phi parameters (MSci model) for BDI events always correspond to the
  horizontal branches
• MSci generator syntax accepts source branch first, then target branch
• MSci generator prints phis on horizontal branches for BDI events
• Numbering of loci in load balancing stats output starts from 1 instead of 0
• Removed checks for consecutive unary nodes which fixes the rejection of some
  correctly constructed MSCi newick formats

• Failing assertion caused by trying to update a non-existent root branch
  length for circle/triangle/square nodes in species tree spr with relaxed
  clock
• Error message in simulation for locusrate syntax
• MRCA function (for MSCi) in gene tree age proposal to find the MRCA
  population of two daughter nodes (a and b), such that the MRCA is also a
  descendant of the population of the parent of a and b. This fixes a failing
  assertion
• Rule in MSCi creator that prevented from having multiple bidirections on
  sister species
• Header of modelparafile when using relaxed clock models (printing of species
  tree branch rate labels)
• Removed SNL branch rate swap strategies when species tree root changes
• Removed branch rates swapping from sSPR and SNL when move is NNI

• Zig-zag load balancing scheme
• Removal of sequences that contain only missing data
• Gene tree topology change move using simulation (option --exp_sim)
• Gamma prior for tau
• Gamma and Beta for theta

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